Hi,
I am quite new to NGS sequencing and have some issues with my data analysis. I sequenced 160 biological samples using MiSeq (18S RDNA), each with one technical replicate, meaning I used DNA from one sample twice, resulting in 2 samples per animal.All were sequenced on the same lane.
I used the Qiime pipeline to analyse the data down to an OTU table, because I want to look for certain parasites.
Now I am not sure what to do with the technical replicates as they are somehow pseudoreplicates. If I look at specific OTUs and compare the read number between the two, they differ from each other. What do I do now? If I average them, a lot of information gets lost, but I´m not sure if I can simply sum them up per OTU. I read the paper of Marioni et al,2008, but I`m still not sure if its really dealing with the same problem, because it compares different lanes.
Does anyone have any suggestions?
Thank you